Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate WP_032992849.1 RL_RS20700 phosphoglycerate kinase
Query= BRENDA::P36204 (654 letters) >NCBI__GCF_000009265.1:WP_032992849.1 Length = 419 Score = 338 bits (868), Expect = 2e-97 Identities = 180/384 (46%), Positives = 245/384 (63%), Gaps = 2/384 (0%) Query: 10 DLKGKRVIMRVDFNVPVKDGVVQDDTRIRAALPTIKYALEQGAKVILLSHLGRPKGEPSP 69 D++GKRV++RVD NVPVKDG V D TRI PTI E+GAKVILL+H GRPK PS Sbjct: 30 DIRGKRVLVRVDLNVPVKDGKVTDVTRIERVAPTILELSEKGAKVILLAHFGRPKDGPSS 89 Query: 70 EFSLAPVAKRLSELLGKEVKFVPAVVGDEVKKAVEELKEGEVLLLENTRFHPGETKNDPE 129 + SL+ +A + E+L V +G+ AV + +G++LLLENTRFH GE ND + Sbjct: 90 DLSLSLIAPSVEEVLDHAVLTASDCIGEAAASAVAAMNDGDILLLENTRFHKGEENNDSD 149 Query: 130 LAKFWASLADIHVNDAFGTAHRAHASNVGIAQFIPSVAGFLMEKEIKFLSKVTYNPEKPY 189 K A+ DI+VNDAF AHRAHAS G+A +P+ AG M+ E++ L K +P +P Sbjct: 150 FTKALAANGDIYVNDAFSAAHRAHASTEGLAHHLPAYAGRTMQAELEALEKGLGDPARPV 209 Query: 190 VVVLGGAKVSDKIGVITNLMEKADRILIGGAMMFTFLKALGKEVGSSRVEEDKIDLAKEL 249 V ++GGAKVS KI ++ NL++K D ++IGG M TF+ A G VG S E D + AK++ Sbjct: 210 VAIVGGAKVSTKIDLLMNLVKKVDALVIGGGMANTFIAARGTNVGKSLCEHDLAETAKQI 269 Query: 250 LEKAKEKGVEIVLPVDAVIAQKIEPGVEKKVVRIDDGIPEGWMGLDIGPETIELFKQKLS 309 + +A G I+LP D VIA++ + G + V I + IP M LD+GP+++E + Sbjct: 270 MIEAATAGCAIILPEDGVIAREFKAGAANETVDI-NAIPADAMVLDVGPKSVEAINAWIE 328 Query: 310 DAKTVVWNGPMGVFEIDDFAEGTKQVALAIAALTEKGAIT-VVGGGDSAAAVNKFGLEDK 368 A T+VWNGP+G FEI F T A A T G +T V GGGD+ +A+N G+ D Sbjct: 329 RAATLVWNGPLGAFEIGPFDAATVAAAKYAAGRTIAGKLTSVAGGGDTVSALNHAGVADD 388 Query: 369 FSHVSTGGGASLEFLEGKELPGIA 392 F++VST GGA LE++EGKELPG+A Sbjct: 389 FTYVSTAGGAFLEWMEGKELPGVA 412 Lambda K H 0.317 0.137 0.386 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 592 Number of extensions: 29 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 654 Length of database: 419 Length adjustment: 35 Effective length of query: 619 Effective length of database: 384 Effective search space: 237696 Effective search space used: 237696 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory